vibs is a small Perl script that reads the optimized Cartesian
coordinates and normal mode displacements from a Q.Chem or ACES
output and generates a series of displaced Cartesian coordinates
spanning one period/cycle of that normal mode. It is located at
/usr/local/vibs.

Molekel is a molecular visualization program just like JMOL. It
is used here because it can easily generate/export sharp images.
It is located at /usr/local/molekel.

Makempeg is a simple shell script (that someone wrote) to take
a series of JPEG files and turn them into an MPEG movie.
It calls mpeg and ppmtoyuvsplit,
which we have at /usr/local/bin.

Procedure 1. Use the script vibs to generate Cartesian displacement
that get written to an XYZ file.

Example: To generate Cartesan displacements of the 12th
mode from file freq.out, the commandline input would be
vibs freq.out 12
This generates a file called mode12.xyz

2. Open the newly generated Cartesian displacements file by running
molekel. This is done by right-clicking and selecting
the file through 'LOAD>MULTIPLE STRUCTURE XYZ'.

Once you orient the
molecule into a certain position, right-click and select 'RENDER'.
Set the parameters you want and make sure you select 'structure animation'
in the 'action' section and click 'ok'.

In the next window, you would
give a base name for the images that you would ultimately stitch into
a movie.

3. Now comes the real movie-making part and we will use the
makempeg script for that. You can type
makempeg --help to view the usage information.
Typically, if one generated 20 cartesian displacement using
vibs and gave the basename basename in
Molekel your commandline prompt would be

makempeg -fs 1 -fe 20 -fi 1 -base basename

This will generate a movie named basename.mpg. If
something fails, you must be missing one of many executables
(ppmtoyuvsplit, mpeg) that makempeg
script uses.

Now you can see your movie using any movie player. A simple tool
for Linux users would be plaympeg. To play a movie
named basename.mpg in looping mode, your commandlike
input would look like plaympeg -l basename.mpg

Making GIF Animations of Vibrational Modes

What is needed?

vibs is a small Perl script that reads the optimized Cartesian
coordinates and normal mode displacements from a Q.Chem or ACES
output and generates a series of displaced Cartesian coordinates
spanning one period/cycle of that normal mode. It is located at
/usr/local/vibs.

Molekel is a molecular visualization program just like JMOL. It
is used here because it can easily generate/export sharp images.
It is located at /usr/local/molekel.

Gifsicle is a
UNIX command-line tool for creating, editing,
and getting information about GIF images and animations.
We have it locally at /usr/local/bin.

Convert is a fairly standard part of the ImageMagick package that
is used to convert between different image formats, JPEG to GIF in our case.

Procedure 1 - 2. The first two parts are the same as the above section.

3. Once you have your JPEG images, you would want to convert them into
the GIF frames and then a GIF animation.

To convert the JPEGs into GIFs, you run convert [options] *.jpg *.gif

Once you have all your GIF frames, you can use Gifsicle to stitch
them together into an animation.gifsicle --loop *.gif > animation.gif

You can automate the process using a simple Perl script like this one.
#!/usr/bin/perl -w
#######################################################
# Makes GIF animations
# 'convert' converts the JPEGs to GIFs
# 'gifsicle' joins the GIFs into an animation
#